Well, all she does is turn back to normal Samus without any upgrades. I think she should either come back with armor and weapon upgrades or come back in Hypermode. This is how I would work it out.
If she came back with armor upgrades, this would be her special move set:
Up B: Psudeo Screwattack (Slightly stronger and more agile)
B: Plasma Beam (Damages multiple enemies with one shot by traveling through all of them, but only if charged half way or more)
Side B: Super Missiles (Slightly stronger, and somewhat faster)
Down B: Power Bomb (Stronger, but takes a while to blow up and you can only drop one at a time)
And this is if she comes back in a temporary Hypermode:
Up B: Hyper Screwattack (Basically like screwattack, except a lot stronger. This move is executed twice as fast. Also your normal jumps and double jumps act as normal screwattacks. Think of it as a Space Jump/Screwattack combo, only in Hypermode)
B: Hyper Beam (A powerful attack that multiple enemies with one shot by traveling through all of them. If you release the B button after fully charging the attack, you will fire a long stream of phazon [which lasts 3 seconds]. While firing the long beam, tilt the control stick to aim.)
Side B: Hyper Missile (A powerful missile, shoots very fast)
Down B: Hyper Bomb (Electricute people in your range)
What do you think?